I had the advanced phone prep on my GTD, absolute waste on money, though the climate screen on the GTD is great, as the diesel engine takes so long to warm up, unlike the GTI, which takes a minute or two.
Like you I tried the phone in the holder in the centre armrest, and never made signal strength any better, so just left the phone either in my pocket, or somewhere else in the car, and never suffered any problems.
I don't have it now in my current GTI, and you wouldn't know any difference.